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Old 07-06-2015, 11:55 AM   #1
Bachbioinfo
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Default pblat empty output

Hi,

I have a single computer with multiple cores, I use pblat at http://icebert.github.io/pblat/

I got only empty temp files as well as empty outpout

I really do not understand what is the nature of the problem, I think a memory problem

I run it like following : nohup `sudo ./Jobs_pblat.sh` &

the Jobs_pblat.sh contains : $PRGEXEC/pblat -threads=12 -prot -trimT -out=blast9 -minIdentity=25 $DB/db.faa $INFILE/"Orfs.faa" -out=blast9 $RESULTDIR/"Orfs_blat_outblast9_results.out"

Anybody has the same issue with pblat

Thanks for reading my thread
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Old 07-06-2015, 11:58 AM   #2
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Has this worked before or this is the first time you are using this program?
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Old 07-06-2015, 12:01 PM   #3
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Is the first time I used It
I tried parallel blat (pblat ) and blat, I got the same behaviour
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Old 07-06-2015, 12:05 PM   #4
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Can you take a few sequences from each file and run them against each other using blat/pblat to ensure that you have a working program before trying to tackle the full dataset?

BTW: Why are you adding sudo to your job?
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Old 07-06-2015, 12:38 PM   #5
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With a small number of sequences it works fine
I think my database is huge (38 G) may I have to divide my database into several parts and do several blat

thanks again for advices
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Old 07-06-2015, 02:54 PM   #6
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Or you could reverse the roles and make the database into query.
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Old 07-07-2015, 05:30 AM   #7
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It works too ! thanks
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